This is the README for the models associated with the paper:

Eyal G, Verhoog MB, Testa-Silva G, Deitcher Y, Lodder JC,
Benavides-Piccione R, Morales J, De (2016) Unique membrane properties
and enhanced signal processing in human neocortical neurons. Elife

The files here can be used to re generate Eyal’s et al. figures 1 and
3.

All rights are reserved to Guy Eyal, the Hebrew University. 

Abstract:

The advanced cognitive capabilities of the human brain are often
attributed to our recently evolved neocortex. However, it is not known
whether the basic building blocks of human neocortex, the pyramidal
neurons, possess unique biophysical properties that might impact on
cortical computations. Here we show that layer 2/3 pyramidal neurons
from human temporal cortex (HL2/3 PCs) have a specific membrane
capacitance (Cm) of ~0.5 µF/cm2, half of the commonly accepted
“universal” value (~1 µF/cm2) for biological membranes. This finding
was predicted by fitting in vitro voltage transients to theoretical
transients then validated by direct measurement of Cm in nucleated
patch experiments. Models of 3D reconstructed HL2/3 PCs demonstrated
that such low Cm value significantly enhances both synaptic
charge-transfer from dendrites to soma and spike propagation along the
axon. This is the first demonstration that human cortical neurons have
distinctive membrane properties, suggesting important implications for
signal processing in human neocortex.

This directory includes:
1. Data of HL2/3 PCs:
	a. Morphologies of six HL2/3 PCs.
	b. Voltage transients from these six cells

2. Detailed Models that were fitted to match the experimental traces

3. Scripts to run the models and re create the figures in Eyal et al.

To run the scripts you must:
1. Install NEURON (https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide.html)
2. Install the following python libraries:
	a. numpy 
	b. matplotlib 
	c. neuron 
3. I recommend the use of ipython to best display the figures

contact: guy.eyal at mail.huji.ac.il

Examples of running the model:
------------------------------
Instructions are provided below for unix/linux. Please see
https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide.html
for additional help on how to run under windows or on the mac.

Change directory to Fig1 and compile the mod files by typing on the command line:

cd Fig1
nrnivmodl ../mechanisms

Start the simulations with commands like:

ipython -i Fig1a.py

Running the above and similarly with Fig1b.py, Fig1cd.py should produce the following:

Fig 1a inset

Fig 1a

Fig 1b

Fig 1cd


When running Fig3 simulations you can cd to the Fig3 sub-folders and for
convenience recompile the mod files

cd ../Fig3/Fig3a
nrnivmodl ../../mechanisms

Then start with a similar command as before
ipython -i Fig3a_apic_synapse.py

(and similarly for the other programs)

Fig 3a

Fig 3a bottom

Fig 3b

Fig 3c